Add unique naming for FreeBayes and GATK hard filters to avoid losing unique filters during merges. Thanks to Severine Catreux
Delly filters based on high quality variant pairs: performs sample based filtering using parameters tuned to NA12878 structural variant calling
Upload structural variant calls in final output directory using same approach and naming as SNP/indels
Use sambamba with support for regional retrieval using a BED file to avoid command line length issues. #386
Ensure retrieval of samples from cn.mops combined output when sample names are numeric and R adds an X prefit on output to BED
Add base support for latest Zebrafish genome build: Zv9
Document process for adding new organism support to bcbio-nextgen
Fix variant region selection parameter to be compatible with bcftools rc8. Expose provenance.do functionality for finding bash
Ensure non-overlapping read names on CRAM to fastq preparation using sequential part-based naming. Write steps as shell script and run in serial to avoid open file handle errors for large inputs.
Update variant calling pipeline overview to be up to date with current approaches
v0.7.9 release
Improved parallelization and resiliancy for CRAM to fastq conversion. Handles partial failures and provides better cleanup post-merge
Fix bug where we incorrectly add installational base directory to non-java bcbio_system components like the temporary and log directories. Thanks to Karl Gutwin
Generalize support for SGE to enable runs on systems without default queues. Thanks to Karl Gutwin.
Provide documentation for new SGE options
Merge excessive coverage regions into nblock regions instead of applyg post-merge to avoid large numbers of small parallel blocks #386
Improve regional splitting on organisms with large numbers of reference chromosomes to avoid excessive numbers of split regions. #386
Add sample configuration BED output file for delly, mapping samples to IDs. Can be used for delly to VCF conversion and generally useful for interpreting output
Ensure tool directory passed to data upgrade to enable creation of Picard/GATK sequence dictionaries
Add ensemble summary BED file of structural variant calls from multiple callers. Provides method to assess potentially rearranged regions with links to caller evidence.